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Large-scale farming of Undaria pinnatifida is conducted in northern China. Conspicuous natural populations of this alga are distributed on rocky shores in this region. However, the genetic relationship between U. pinnatifida from China and native populations in other countries remains largely uncertain. We obtained sequences for the mitochondrial cox3 and tatC–tLeu regions and the internal transcribed spacer one of nuclear ribosomal DNA from representative natural and farmed populations of U. pinnatifida in China. We analyzed genetic diversity, and evaluated the genetic relationship between Chinese populations and Japanese and Korean populations. The mitochondrial and nuclear DNA sequences revealed high genetic diversity in most Chinese populations. Unique mitochondrial haplotypes were detected in the Gouqi Island population consistent with historical records of a native population on the island. Phylogenetic analyses derived from the mitochondrial DNA sequences revealed that the Chinese samples were classifiable as the Continental and Northern Japan types. All natural populations from rocky reefs in northern China were grouped with the Continental type and all farmed populations with the Northern Japan type. Mitochondrial and nuclear DNA sequences revealed significant genetic differentiation between the farmed populations and adjacent natural populations from rocky reefs, in agreement with previous results obtained using microsatellites. [ABSTRACT FROM AUTHOR]